Well it's an interesting little story you've got there, and the way you ended it will leave people wanting to read what happens next. But can I offer you a little constructive criticism for the next chapter?

geonosis 100 hours."general. clone. number 5881. codename: commander omega."said the super battle droid.
"good......*cough*send him to the detention center." said a large part human part droid being.
where in the love of mandalore were rapier, junga and slashburn?"hey wake up. where is your camp?"
"why would i tell some dirty scrap like you?"said commander. suddenly, a distinct hum filled the air. a bald man stood in the room. he swung his violet blade at the battle droid who was interrogating him. "clone! what are your codes?" demanded the jedi.

"omega squad. numerical 5881. commando commander."

"where is your squad?" asked the jedi as he shut down the ray sheild.

"no clue. split up during capture."

"then forget them. i am mace windu."

"no way. i am taking a gunship to find them."

"are you questioning a direct order?"
"find that out on your own did ya? thought jedi were supposed to be smart."

Great story! Although 2 things: As LordOfTheFish said, Omega Squad already exists. And, about the grammar...... (Do not open the spoiler if you do not want to hear about it)

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Grammar notes: You only used capitals when they yelled when you should use them at the start of names, sentences, and places! Also, the quotation marks. Not much of a problem, but I noticed that sometimes, you did this: "*text*" yelled commander" *text*"
Correct way: "*text" yelled commander. "*text*"
Looks at the differences at the 'yelled commander' part.

But enough of my grammar gibberish ()! I never though of what would happen if a clone was captured....

Over the skies of geonosis a republic gunship flew in search of the remainder of gamma squad............

"Forty-Six, look. a droid outpost heavily guarded by rapid gun turrets, battle droids, and super battle droids. take me there." said commander. the clones 46 and 53 fired the guns, taking out the turrets. commander hit the rocky geonosian ground, rifle in hand, on bolt action mode. "TAKE THIS YOU PEICES OF FILTHY JUNK!!!!!!!!!!!!!" screamed commander, as he shot the battle droids. suddenly, droidekas appeared. " i know how to improvise, trash!" he yelled throwing an emp grenade and running behind a boulder. he ran up to the super battle droid, bashing it 5 times with his gun. "DIE!!!!!!!!!!!!!!" he screamed, pushing a grenade into the chasis. suddenly, the large droid exploded. he placed an explosive on the ironclad door. within 5 seconds the door exploded. "get him!"
"I DON'T THINKS SO!!!!!!!!!!!" shouted commander as he threw he gun hitting three droids, and took out his dual pistols shooting the other five. within an hour he was in the controll room, accessing the base schematics. "prison block is westward..the vent pipes lead straight to it.... let's go." the vents overhead led to the westward cell block. an executioner droid was working the console. "where is your base?!!!"
" on al-" said junga
"deathrow!" yelled commander kicking the vent plate as it hit the droid on the head. "someone order death?" laughed commander as the escaped the facility.

Onderonian skies: 1200 hours
in the cruiser estenance, commando squad gamma was preparing for their next mission.......

"alright squad, just got words from the jedi. onderon is being held hostage by general greivous and his droid armies. republic forces are going to battle droid opposition. we shall take the palace." breifed commander " oh, and watch out for tanks. we do NOT want another geonosis."

it was pure chaos on onderon. scrap and blood everywhere. "junga! proceed with anti-armor!" yelled slashburn. overhead, rapier and commander were on flying drexl beasts, shooting down CIS gun emplacments. suddenly, an AAT exploded along with 5 sbd's. the two flying beasts landed. "thank you republic soldier. onderon forever owes you." said an onderonian captain.
"captain. give your troops guns and accompany junga and rapier. they know the plan. slash and i will take the western flank of the palace. you will go east. master yoda will go head on." said commander. the onderonian liberation had begun.

"slash! take out that tank!" screamed commander, as he was dealing with battle droids. he slammed the heads of the droids together due to his lack of ammo. it was worse for junga and rapier however............
"darn it! reload you scrapper!" screamed junga. the droid opposition was overkilling the troops. "captain! support!" screaamed rapier. the onderonian captain raised his loaded rocket launcher at the ceiling and fired. the commandos were trapped without ammo with 20 SBD's.

eventually the republic took iziz, onderon's lone city.
"CAPTAIN! WHERE ARE JUNGA AND RAPIER?" shouted commander.
"they....have been removed." said captain with a slimy smirk on his face.
"scum!" said commander punching the onderonian captain in the face. "the worst offense in my book is to betray a friend. the penalty-death." said commander shooting the downed captain.
"so? what we going to do?" asked slashburn.
"obviously we are going after them. to utapau."

"this is crazy! we cannot just go barging into a sep base!" screamed slashburn.
"what did i tell you was the worst crime in the galaxy?" asked commander.
"betrayal. second worst being deserting a friend."
"now you know why we are-"
"sep cruiser. the decimator. ventress' ship."
"let's use capture counter 89."
meanwhile on utapau...........................

"guagh!!!!!!!!!!"screamed rapier. fifteen syringes filled with torture serum were in his arm."you'll never get anything outta me. sith scum!"
"yes. well perhaps you will end up like your friend over there."said sidious, pointing to junga's dead body. the quad squad was a trio task force.

"clones are all to be killed as of today. time to die." said asajj ventress
"no. i do not think that will work out for sith trash." said commander, shoting her with his grenade launcher while slash fired his machine gun. within minutes, the decimator was destroyed. without the clones or their ship: the courier.

utapau 1200 hours

"take the comlink. you will have to take out the AD cannons for me to take out greivous' ship. once they are out of the way, i can bomb the towers."
" fly low. contact kenobi."
"good luck commander."
"not luck. pure skill and resolve."

shells and blood all over. that was always commander's life-shells and blood. now that he felt the cold, all he had to live on was his morale. no man left behind. all who get in the way are to be killed. ahsoka tano was an example of that rule. as was the onderonian captain who left his brothers to die.

"commander cody........come in."
"yes commander gamma?"
"i want you to blast the bays. i will enter west into the torture room. kenobi will search for greivous. i envy him. yet, i am here without orders. gamma out."

commander's final stand has begun.

the droids battled furiously with the clone opposition. obi-wan was holding off general greivous. slashburn fought droid fighters. the 501st had taked down the anti-air flaks. the war was in its climax. commander of omega squad was unbeknowest to it all.

""there he is! get him!" screamed a magnaguard.
"WHERE IS RAPIER!!!!!!!!!!!!!!!!" screamed commander grabbing the shockstick, spliting it in two and kicking the droid off the platform into the endless sinkhole.

the torture room was littered with bodies and splatterd red of blood. then commander saw the worst sight he could of thought of: rapier near dead and junga's dead corpse.
"who goes there?" said a familiar voice." it was rapier.
"it's me. commander. you're goin home."
"thank mandalore."

rapier and slashburn off planet, only left assisting kenobi. he walked seeing kenobi being shot at by clones. order 66.

"NOOOOOOOOO!!!!!!!!!" yelled commander firing at the soldiers.

"all the other clones were firing. why not you?" asked kenobi as they escaped utapau.
"after today, i am not a clone." said commander. "my name is now nikkon."

commander was shot by a sniper on yavin 4.
slashburn was killed during the hoth invasion.
rapier died during the destruction of the 1st death star. this is the end.